The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

Abstract

BackgroundTheobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.ResultsWe describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation.ConclusionsWe report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

“…2b). Based on the phylogenetic tree constructed using 6,911 orthologous gene families from Theobroma cacao 27 , G. raimondii 4 , G. arboreum 2 and the two subgenomes of G. hirsutum, the evolution rates of homologous genes were estimated for each branch (Supplementary Fig. 9a).…”

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

“…We demonstrate how these differences in sample-wide LD can practically impact the resolution of association mapping analyses. Using microsatellite haplotypes and phenotypic data on pod coloration, a wellunderstood cacao phenotype (Marcano et al 2008;Motamayor et al 2013), we show how association mapping analyses are far less precise in an F1-mapping population from Brazil (referred to as MP01) compared to a semi-cultivated population from Hawaii (referred to as Hawaii). Finally, given the existence of varying levels of LD in wild and cultivated cacao varieties, we highlight how careful sample selection will be a crucial factor in the efficacy of future association mapping analyses.…”

“…The linkage mapping studies that have been carried out in cacao have concentrated on mapping QTL within F1 or F2 mapping populations. While this work has been valuable in identifying some QTL in the cacao genome (see Lanaud et al 2009;Motamayor et al 2013;Royaert et al 2011;Schnell et al 2007), its effect on cacao breeding and research has been limited by a number of factors. These include small mapping populations derived from relatively heterozygous parents, funding inconsistencies, and the pervasive mislabeling of elite cacao varieties.…”

“…The physical location of each marker loci was determined by comparing microsatellite flanking sequences and their primers against a recently published, high-resolution cacao genome (Motamayor et al 2013) using both BLAST and e-PCR (Altschul et al 1990;Schuler 1997). All base-pair positions reported in this study indicate a physical location on this reference genome, which was built from the Matina 1-6 cultivar, the most common cultivated type of cacao and belonging to the Amelonado diversity group (Aikpokpodion et al 2009;Efombagn et al 2008;Motamayor et al 2013Motamayor et al , 2003. These physical locations are consistent with their locations on a previously published composite genetic map .…”

Plant genomics: sowing the seeds of success

“…Unfortunately, the blending of cacao reduces the overall quality of chocolate. Motamayor et al [20] generate a high quality genome sequence of Theobroma cacao cultivar Matina to improve the speed and accuracy of cacao breeding. Utilizing the genome sequence in conjunction with a haplotype-based method, they identify the TcMYB113 gene, which encodes an R2R3 MYB transcription factor, as a likely candidate for controlling red/green pod coloration: higher expression of TcMYB113 is associated with red pod color.…”